Compared with LC patients, PON1_N253 (H5N4S2) and HPTR/HPT_N126/184 (H5N4S1) were significantly up-regulated in AFP-negative HCC (p = 0.0026 and p = 0.0366, respectively), while APOH_N253 (H5N4S2) was considerably decreased (p = 0.0127). This evidence concerns the gene PON1 and hepatocellular carcinoma.